Act three begins when the Sole Survivor acquires the ability to fast-travel to and from the Institute at the end of Institutionalized. At this point, the main quest's structure splits into four different branches, one for each of the four main factions. Certain events in those factions' quests can make other factions hostile to the Sole Survivor, thus locking them from those branches and failing all of that faction's on-going quests. In some situations, this can be delayed (or even accelerated) with certain actions or certain dialogue choices.

Should the player decide to oppose the Institute by supporting any of the other three factions, the main quest ends with The Nuclear Option quest (there are actually three variants of the same quest, one for each faction opposing The Institute). However, should the player join and support The Institute, the main quest ends with the Nuclear Family quest.

The following quests become available after completing Institutionalized:

The Brotherhood of Steel, the Institute, and the Railroad are mutually hostile. Progressing through one's questline will eventually make the player hostile to the other factions.

Siding with the Institute might make the Minutemen hostile, but this can easily be avoided with Charisma checks and selecting the correct dialogue choices.

The Minutemen route only becomes available if the player character is hostile with the Institute, either by attacking them or by getting into a heated argument with Father. If the player character wishes to end the main quest by siding with the Minutemen, the Institute is the only faction that needs to be destroyed.

The Minutemen can also become hostile with The Railroad if they don't sound the evacuation signal during the Nuclear Option quest.

The Minutemen can also destroy the Brotherhood of Steel if they later get into a hostile relationship with the player character, even if the player character sided with the Brotherhood in order to finish the main quest.